PALEOMIX v1.2.13

Added

• Added 'retable' command for pretty-printing whitespace separated data in
  the previously used by the BAM pipeline.
• Basic statistics are collected for pre-trimmed reads in the BAM pipeline.

Changed

• BAM pipeline tables are now saved as tab separated columns. The old
  pretty-printed format may be produced by running the 'retable' tool on
  the resulting files.
• Memory usage for the 'coverage' and 'depths' commands were reduced when
  using very big BED files.

Fixed

• Fixed input / output files not being listed in 'pipe.errors' files.
• Use the same max open files limit for picard (ulimit -n minus headroom)
  when determining if the default should be changed and as the final value.
• Removed explicit test for JRE version, which was failing on some (valid)
  runtimes. Java programs are still checked prior to running pipelines.
• Fixed changes to recent version of Pysam breaking the alignment step
  in the BAM pipeline.
• Fixed various test failures resulting in different environments.
• Fixed validation of pre-trimmed FASTQ files in BAM pipelines stopping
  early if empty files are encountered.

Removed

• Removed automatic migrating of configuration files created PALEOMIX
  PALEOMIX prior to v1.2.0.
• Previously deprecated support for existing BAM files was removed from
  the BAM pipeline.